Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_024487810.1 C1M55_RS08415 acyl-CoA oxidase
Query= BRENDA::Q33DR0 (703 letters) >NCBI__GCF_002893965.1:WP_024487810.1 Length = 643 Score = 494 bits (1271), Expect = e-144 Identities = 272/623 (43%), Positives = 371/623 (59%), Gaps = 2/623 (0%) Query: 43 GRWADIRLHARDLAGREVVQKVEGLTHTEHRSRVFGQLKYLVDNNAVHRAFPSRLGGSDD 102 GRW ++R R E RS+ Q++ L D F GG+ D Sbjct: 14 GRWREVRERVRGELNDERFAPHYTPNTAIARSKALEQMRVLADLGYAANGFAVSHGGTGD 73 Query: 103 HGGNIAGFEELVTADPSLQIKAGVQWGLFGSAVMHLGTREHHDKWLPGIMSLEIPGCFAM 162 GG + E L +D SL +KAGVQWGLFG A+ +LGT HH ++ ++ L++ GCFAM Sbjct: 74 AGGAVTSIEMLAMSDLSLMVKAGVQWGLFGGAIENLGTERHHQAYVKPLIDLDLLGCFAM 133 Query: 163 TETGHGSDVASIATTATYDEETQEFVIDTPFRAAWKDYIGNAANDGLAAVVFAQLITRKV 222 TETGHGSDV + TTATYD ET EFV+++P ++ KDYIG AA A VFAQLIT Sbjct: 134 TETGHGSDVQELETTATYDVETGEFVVNSPTPSSRKDYIGGAAQHATVAAVFAQLITGGE 193 Query: 223 NHGVHAFYVDLRDPATGDFLPGIGGEDDGIKGGLNGIDNGRLHFTNVRIPRTNLLNRYGD 282 + GVH F V +RD A D LPG+ D G+KGGL G+DNGR+ F VRIPR NLLNRY D Sbjct: 194 SQGVHCFVVPIRDDAGND-LPGVTTSDCGLKGGLPGVDNGRIVFDQVRIPRENLLNRYAD 252 Query: 283 VAVDGTYSSTIESPGRRFFTMLGTLVQGRVSLDGAAVAASKVALQSAIHYAAERRQFNAT 342 VA DGTYSS IE+P RRFFTM+GTLV+GRV++ G+A AA++V L A YA +RRQF+A Sbjct: 253 VAEDGTYSSAIENPNRRFFTMVGTLVRGRVTVGGSAAAAARVGLAIAGRYALQRRQFSAP 312 Query: 343 SPTEEEVLLDYQRHQRRLFTRLATTYAASFAHEQLLQKFDDVFSGAHDTDADRQDLETLA 402 +E +++DY HQ+RL +A +YA FA +L+ D+ S ++++LE A Sbjct: 313 KSDDEVLIMDYLVHQKRLLPLIARSYALQFAQNELVAAMHDIQSSDDPDPQEQRELEGRA 372 Query: 403 AALKPLSTWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKR 462 A LK +TWHA +QE REACGGAG+L ENR +L+AD DV+ TFEGDN VL QLVAK Sbjct: 373 AGLKAANTWHATRAIQEAREACGGAGYLAENRLTALKADTDVFTTFEGDNHVLTQLVAKE 432 Query: 463 LLADYAKEFRGANFGVLARYVVDQAAGVALHRTGLRQVAQFVADSGSVQKSALALRDEEG 522 LL YA E RG + R+ + V RT +Q+ Q + D+ + +L + Sbjct: 433 LLTSYADEVRGMSPVDWMRFAATTVSDVVKKRTAAQQILQTIVDTRQDNEEDGSLFNRGT 492 Query: 523 QRTLLTDRVQSMVAEVGAALKGAGKLPQHQAAALFNQHQNELIEAAQAHAELLQWEAFTE 582 Q + DR + ++A L+ A K ++ A FN Q+ +++AAQAH E + EAF Sbjct: 493 QMKMFEDREEYLLATAARRLQAAQKREENPFDA-FNFVQDHVLKAAQAHIERVILEAFVA 551 Query: 583 ALAKVDDAGTKEVLTRLRDLFGLSLIEKHLSWYLMNGRLSMQRGRTVGTYINRLLVKIRP 642 + +D KE+ + DL+ LS+IE+ +W++ + LS++R + V IN +RP Sbjct: 552 GIDSCEDETAKELFGEVCDLYALSVIEEDKAWFMEHRHLSVERSKAVTRGINERCRTLRP 611 Query: 643 HALDLVDAFGYGAEHLRAAIATG 665 H L+D FG L +A+ G Sbjct: 612 HVETLIDGFGIPDILLGSAMLDG 634 Lambda K H 0.319 0.134 0.387 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1010 Number of extensions: 45 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 703 Length of database: 643 Length adjustment: 39 Effective length of query: 664 Effective length of database: 604 Effective search space: 401056 Effective search space used: 401056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 54 (25.4 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory